Ends and Means
by MsRaven
Summary: Post-Ep for Childhood's End. Sheppard gets a dressing down from Weir about what happened back on the planet. Then something unexpected happens. WeirSheppard eventually.
1. The Argument

**Ends and Means**

**Summary: ** Post-Ep for Childhood's End. Sheppard gets a dressing down from Weir about what happened back on the planet. Then something unexpected happens. Weir/Sheppard.

**Spoliers: **Everything up to Childhood's End.

**Disclaimer:** Stargate Altantis and its characters do not belong to me.

**Author's Notes:** What can I say, I'm on a roll. Either that or I have too much time on my hands. This continues in the same storyline as my other FF, but you don't really need to have read them to get this one. Anyway...I don't see Sheppard as the type of person to take criticism well, so this starts with my take on his reaction to Weir's disapproval.

_ Thanks for all the reviews on my previous stories. I'm still working on catching all my verb tense mistakes, so please bear with me. _

Major John Sheppard and the rest of his team are back in Atlantis. They're in the middle of the briefing and he can't keep himself from tuning out as Rodney McKay goes on and on about how he fixed and improved the electromagnetic shield. He doesn't know how Ford and Teyla can look attentive because they were all treated to McKay's explanations on the flight back to the gate. He notices a small mistake in McKay's calculations, but chooses not to call him on it. (The shield is actually 54.3% bigger than it was before.)

He decides, instead, to focus on his new favorite hobby – the beautiful Dr. Elizabeth Weir. It's been a few weeks since they had their little "run-in" down in the lower levels. He knows what he wants, but figures that convincing Elizabeth is going to take a little more time. She's been building some pretty high walls around herself since accepting this position. John's plan is to chip his way slowly through those walls and be entrenched before she knows what hit her. His standard MO of piling on the charm will probably just freak her out.

She's sitting across the conference table from him, facing McKay who is presenting at the end of the table. Since he's supposed to be listening too, John can only glance at her out of the corner of his eye. He notices that she looks tired. Then again, she has every reason to be tired. Running Atlantis on a daily basis would be tiring for even the most experienced commanders.

But today she looks a little worse than normal. He didn't even get the standard "welcome back" smile when they came through the gate. The jumper always hovers in front of the gate for a moment before going up to the bay. All the other times he'd come through, she would give them a relieved smile to welcome them back. But today she had barely glanced up from her conversation with Peter on the command deck.

Weir also isn't saying much during the briefing. She'd looked like she was going to speak up after he gave his mission report, but didn't. It's clear there's something bothering her.

John wonders if Kavanagh is giving her a hard time again. The guy still hasn't gotten over how Weir had put him in his place in front of his team. Kavanagh has a bigger superiority complex than McKay and that was saying a lot. He wonders if he can have a talk with the guy without seeming too over-protective of Elizabeth.

"Thanks Rodney. I look forward to hearing how you plan to incorporate what you learned into increasing our defenses. I think that's all for now. Thanks everyone."

Glad that he doesn't have to listen to McKay talk anymore, Sheppard quickly gets up to walk out of the conference room.

"Major Sheppard. Could you please stay for a moment?"

Everyone in the room stops moving and looks over at Weir.

"The rest of you need to report to the infirmary for your check-ups. Tell Dr. Beckett that Major Sheppard will be along in a few minutes."

His team walks out and Sheppard sits back down. He doesn't know what she wants to talk about, but he can't think of any reason to be concerned. He should have been worried by how nervous McKay looked when he walked out. Even more so when Elizabeth closes the doors behind his team.

Weir sits back down across the table from him. She looks a little pale and leans forward with a serious expression on her face. Sheppard is the opposite. He's leaning back in his chair with a small smile playing on his lips.

"What's up Doc?"

That old WB joke always makes her smile. This time, he gets no reaction. Not even the smallest hint of a smile. She lets out a little sigh and this has Sheppard sitting up in his chair with some concern.

"I wanted to talk to you about how you handled the situation back on the planet."

"What about it?"

"It was irresponsible for you to allow the shield to be dropped and the ZPM brought back to Atlantis."

"Finding energy sources is the reason why we go out there in the first place."

"The shield was the only thing protecting those children from the Wraith."

"We got it back up!"

"Not before a Wraith probe showed up."

"McKay got the shield back up before it could go back through the gate."

"How do you know it didn't transmit before it was taken out?"

"I don't. But it doesn't matter. The shield is back up!"

"That's not the point."

"Then what the hell is the point? Because from how I see it, we ended up saving a lot of lives today!"

"The ends does not always justify the means. You still could have stopped the suicides without endangering the people in the villages. What if Rodney hadn't gotten the shield back up?"

"But he did! What could have happened doesn't matter now!"

"Yes, it does. Don't you see? You intentionally put every person on that planet in danger just to bring a ZPM back to Atlantis. And you were willing to keep it and never put the shield back up."

"We would have brought them back to Atlantis if the ZPM was worth keeping!"

"You can't keep bringing people here."

"Why not? It's worked so far!"

"Because we don't have the resources. Because we're not the Ancients. We can't protect everyone in this galaxy from the Wraith. Not even the Ancients could protect them from the Wraith!"

"But without the ZPMs, we can't even protect ourselves!"

"If we're going to live here, we're going to have to stop believing we're more important than everyone else."

"You know damn well I don't think that way!"

"And yet Rodney still brought the ZPM back to Atlantis."

"Then why aren't you having this conversation with Rodney?"

"Because you are responsible for the decisions that the members of your team make during a mission."

"He'd already taken the ZPM out when he radioed me! He would have done it anyway!"

"Are you saying that you are unable to control the actions of your team?"

"Damn it! That's not what I'm saying!" Sheppard explodes from his chair and glares down at Weir. He slams his fists down on the table and leans forward menacingly. "MAYBE IF YOU GOT OFF YOUR ASS AND WENT THROUGH THE GATE NOW AND THEN, YOU'D SEE WHAT IT'S LIKE TO MAKE DECISIONS IN THE FIELD!"

Weir jumps up and matches Sheppard's glare.

"MAYBE IF YOU STARTED MAKING THE RIGHT DECISIONS FOR ONCE, I WOULDN'T HAVE TO STAY HERE AND KEEP DEALING WITH ALL OF YOUR SCREW UPS!"

They stay like that, glaring at each other for a full minute. Neither of them want to be the one to give in. Eventually Elizabeth leans back and squares her shoulders. She opts to end the confrontation with strength, not weakness.

"That's all for now Major. You're expected in the infirmary. Dismissed."

Sheppard fumes at her not-so-subtle reminder of who is really in charge of Atlantis. He slowly straightens from the table with his eyes flashing with fury.

"Yes - sir." He sneers before turning and storming out of the conference room.

He's too angry to notice that Elizabeth's cheeks were flushed with more than anger. That a layer of perspiration had formed on her forehead. He's too angry to look back and see her double over, no longer able to keep herself upright. He's charging down to the infirmary and doesn't see her clutch at her side. He's too far away to see the pain overcome her before she can call out for help.

There's nobody to see as she collapses and falls to the floor unconscious.


	2. Medical Emergency

**Ends and Means, Chapter 2**

Teyla, Ford, and McKay are just walking out of the infirmary when Sheppard storms past them. He is clearly upset as he disappears into the infirmary.

"Major Sheppard does not look happy."

"I guess that wasn't a good discussion with Dr. Weir."

"Yeah...I didn't think that was gonna be good."

There's something in McKay's voice that make the other two look at him questioningly.

"You know something we don't?"

"Elizabeth was a little upset that I brought that ZPM back to Atlantis."

"I told you that wasn't a good idea!"

"Well I see that now!"

"I don't get what that has to do with the Major."

"He is the leader of our team. Our decisions reflect his leadership."

"So McKay making a mistake means that it's Sheppard's fault?"

"Hey! I was doing it for the right reasons."

Teyla chooses to ignore McKay.

"You forget, Lt. Ford. The major did give McKay permission to return to Atlantis with the ZPM."

"Maybe I should go talk to him."

"Did you see his face McKay? Somehow I don't think you talking to him is a good idea."

"I agree. I think it would be wise for you to avoid Major Sheppard for some time."

"Then I'll go talk to Dr. Weir."

McKay walks away before Teyla and Ford can stop him.

"I do not think talking to Dr. Weir is any wiser than talking to Major Sheppard."

"You're probably right. I'll go stop him."

Ford goes running after McKay. Teyla looks over her shoulder at the infirmary before turning to go back to her quarters.

In the infirmary, Sheppard is soothing his bruised ego by flirting outrageously with one of the nurses. He tells her about what happened on the planet and she is suitably impressed by how many lives he saved by stopping future sacrifices. He doesn't hesitate when she suggests they go grab dinner together.

They're a few corridors away from the infirmary when a frantic sounding McKay is heard over the communications system.

"Medical Emergency! Dr. Beckett to the command deck. Hurry!"

Before anyone can move, another voice, this time Ford's, is heard – only a little less frantic than McKay's.

"Negative! Negative! Scratch that. There's no time. She's burning up! Dr. Beckett, we're coming to you."

Sheppard breaks into a dead run for the infirmary. He gets there just in time to see Ford carrying someone in through the doors. He runs into the infirmary, but Beckett's team is surrounding the bed and he can't see anything. McKay is doubled over near the door trying to catch his breath. Sheppard walks up, grabs his shoulder, and forces McKay to look at him.

"Tell me what's going on!"

But McKay is too winded from his run from the command deck to respond clearly. Sheppard shakes his shoulder hard.

"Say something!"

"Weir." Is all McKay can say through gasping breaths.

Sheppard spins around to face the bed as all color drains from his face. He sees Ford get shoved aside by one of the nurses. He catches a glimpse of Elizabeth when the members of the medical team shift around the bed. She has an oxygen mask over her face and the only distinguishable feature he can make out is her hair that is plastered to her forehead.

Beckett stumbles into Ford and pushes the lieutenant toward where McKay and Sheppard are standing. He walks over, too stunned to notice the distraught look on the major's face. Teyla and Peter walk into the infirmary at that moment. She notices how pale John is and places her hand reassuringly on his arm.

"I am sure she will be fine."

"What-" His voice comes out in a croak and he has to clear his throat before starting over. "Tell me what happened."

"I was trying to stop McKay from going to talk to her." Ford is the first to respond. "I got there just as McKay was walking over to the conference room."

"She wasn't in her office." McKay adds.

"She was lying on the floor in the conference room. It didn't look like she hit her head or anything. She was too far away from the table."

"I called for the medical emergency and Ford went to check her pulse."

"She was burning up pretty bad, so I figured it was better to bring her here instead of waiting for Beckett to get his gear and go up to the command deck."

Sheppard turns to Peter. "Where were you?"

"I was on the command deck, but I didn't notice that she hadn't come out of the conference room after the briefing."

He valued his life, so he didn't add that everyone on the command deck had heard their argument. They couldn't quite make out what they were saying, but they all heard the raised voices. More than a few people were visibly startled by hearing Dr. Weir yell back at Sheppard. When he stormed off, there was nobody willing to risk disturbing Dr. Weir.

They all turn as Dr. Beckett walks over looking very concerned.

"Any of you notice anything wrong with Dr. Weir today?"

They all shake their heads.

"She looked a little pale during the briefing." It's the only thing Sheppard can think of. His team has only been back for a few hours.

"Wait!" Peter suddenly speaks up. "I saw her grab her side earlier today. It looked like she was hurt, but she told me it was just a muscle cramp. I didn't press her on it."

"Which side?" Beckett prods.

"Uh...her right, I think."

"Ya sure?"

"Yeah, yeah. Her right."

At that, Beckett runs back to Weir's bedside.

"I do not understand." Teyla says. Sheppard doesn't get it either.

"Appendicitis?" McKay guesses.

Sheppard relaxes a little at that. Kids get appendicitis all the time and turn out okay. It can't be too bad.

"Oh that can't be good." McKay sounds like he's in physical pain himself.

Sheppard looks up and can barely believe what he sees. Elizabeth's body is convulsing on the bed. Beckett is barking orders at his staff to try and control her fever induced seizure. They need to get it under control before they can prep her for surgery.

John knows that this medical team is top notch. They've already saved his life several times. But he can't help the fear that's coiling in his gut as he sees them wheel Elizabeth into the back surgical area. He's never been more scared in his life.

The others don't stay in the infirmary for too long. There isn't much they can do and they are confident that Beckett will do everything he can for Dr. Weir. Ford stays the longest, standing next to his CO, and trying to provide what little support he can. Ford can only guess at the guilt eating Sheppard up inside.

Eventually Sheppard is the only one left standing vigil in the infirmary. He doesn't notice the nurse he was supposed to have dinner with walk by. She, on the other hand, sees him and knows by the look on his face that she doesn't have a chance with him now. She probably never did.

John is holding onto the last thread of his sanity when they finally roll Elizabeth back out to the main part of the infirmary. Beckett is only slightly surprised to see Sheppard still standing there. He smiles as he walks over to the major.

"She's gonna be fine. We were lucky. There was only a small tear in her appendix and the infection hadn't spread too far. She'll be on some pretty heavy antibiotics for a while though. But she should be up and around in a few days."

"Can I go see her?"

"Sure. She's still under, but it can't hurt."

"Thanks."

John walks over to the bed as Beckett leaves in search of his dinner. Elizabeth still looks pale to him as she lays so still against the white sheets. They're alone in the now deserted infirmary. Not that he notices. He's focused totally on the woman in the bed.

He can only shake his head at the irony of the situation. He's usually the one in the infirmary needing to be worried over. John doesn't like the switch in their positions. Leaning over, he places a soft kiss on Elizabeth's forehead that is still warm with a slight fever. As he moves away, he whispers a soft command.

"Don't ever make me go through that again."


	3. Breakout

**Ends and Means, Chapter 3**

Dr. Elizabeth Weir has now been in the infirmary for three days. It's actually been four days since her collapse, but she isn't counting the day she spent mostly unconscious after emergency surgery on her appendix. She feels a little sheepish that, with the all the dangers they've encountered in the Pegasus galaxy, she manages to get laid out by an infected piece of non-essential intestine.

She hates infirmaries and hospitals and clinics. It's not that she fears for herself. Needles and scalpels don't bother her. She's been to too many hospitals in her years of brokering peace in third world countries. From the small huts which held starving children to the larger buildings filled with wounded soldiers, she has learned to hate them all. They remind her too much of the friends she has lost. This room reminds her that her most challenging goal of this expedition is to keep her team out of this infirmary.

Elizabeth wakes from a short nap to find the infirmary empty except for a nurse in the far corner. In truth, she has not been given much opportunity to dwell on her dislike of infirmaries. She realizes that this is the first time she hasn't woken up to two members of her team arguing about whether they should wake her. She wonders if Beckett has succeeded in locking the doors.

Everyone has tried to chip in and keep Atlantis running smoothly without her up on the command deck. Dr. Beckett gave her strict orders to stay in the infirmary and rest. It was proving to be easier said than done. Much to Beckett's frustration, there has been a constant flow of people through the infirmary during her stay. A lot of her visitors have come asking for advice on one thing or another. But she has also been pleasantly surprised at the number of Atlantis team members who have come just to see how she was feeling. Halling and Jinto brought her flowers from the mainland along with the well wishes of the whole Athosian colony. Elizabeth figures that every person in Atlantis has come by at least once.

_Everyone but John Sheppard._

_He's been busy. Peter told me that he's been coordinating all the gate travel._

_Which means that he hasn't been going through the gate himself. But you still haven't seen him since you've been in here._

_I know._

Elizabeth turns to lay on her side as she lets out a little sad sigh. She didn't want to admit to herself that John's absence from all the other well-wishers had hurt. Ford, McKay, and Teyla had all come by several times. Teyla had even gone to her quarters and gotten her some pajamas to wear instead of the embarrassing hospital gown Beckett had her in after surgery.

_I can't really blame him for staying away. That was a pretty nasty argument that we had._

_Staying away out of spite is kind of childish, don't you think?_

_This is Sheppard we're talking about._

Weir is facing the back wall, so she only hears the infirmary doors open. She refuses to turn around to see who it is. She's given up expecting it to be Sheppard and isn't in the mood to see anyone else. If she pretends to be asleep, maybe they'll go away for once. She waits, but doesn't hear any footsteps and relaxes.

"I know you're awake."

The whispered statement is made from so close that she feels his breath tickle her ear. She turns, startled, to find Sheppard's face only inches away from her own. She considers herself lucky that she's no longer hooked up to the heart monitor that would give away how her pulse is now racing.

"John..."

His smile widens at her use of his first name.

"What-"

He puts a finger over her lips to silence her and looks over his shoulder at the nurse who is engrossed with whatever is on her computer display.

"Shhhh."

"What's going on?" She whispers.

"I'm staging a break out."

He's grinning now, his eyes dancing with mischief.

"What?"

"I know you don't like infirmaries, so I'm here to sneak you out."

She smiles, touched that he remembers that about her. But she's already been ordered to stay an extra day in the infirmary because Dr. Beckett didn't think she was properly resting with all the people traipsing through. She isn't sure she's willing to risk another day.

"Dr. Beckett said that I was supposed to stay here and rest."

"Beckett shmeckett. What does he know?"

"He's the head of the medical team and is the only one that can order me to stay here for another day."

"Okay, so he might know some stuff." John shrugs. "But he said that you weren't getting any rest here anyway. I'm sure he won't mind if I take you somewhere that people can't bother you."

_He talked to Beckett about me?_

She isn't sure if she should be touched or upset.

"I don't know." She tries one final excuse. "I'm not exactly dressed to be running around Atlantis."

"Don't worry. I went to your quarters and got you some clothes."

"What?!"

"Shhh." He looks over at the nurse again. "Okay, so I actually asked Teyla to go get you some clothes. Now here. Change quick."

Elizabeth is out of excuses, so she grabs the bag he hands her and slowly moves off the bed. John is quickly at her side with an arm around her waist to support her.

"Easy there."

"I'm good thanks." She smile up at him. "I'll be right back."

She walks slowly to the rest room to change. In the bag, she finds some of the few casual clothes she brought on the trip. A pair of jeans, a fitted lavender t-shirt, a pair of sneakers, and a light jacket. She notices, as she steps back into the infirmary, that John is wearing similar clothing. He looks like the classic flyboy in his black t-shirt and flight jacket. The half smile completes the picture of a guy who has captured and broken his share of hearts.

_Maybe this isn't such a good idea._

Sensing her hesitation, he grabs her folded pajamas and places them on the bed. Taking her hand in his, he starts to lead her out of the infirmary. They're in the hallway before he stops and jogs quietly back over to the bed. She watches as he pulls a piece of paper out of his jacket pocket and places it on top of her pajamas. He jogs back out to her.

"A note." He motions over his shoulder. "For Beckett. I don't want him too worried."

"You left him a note that says I'm with you? And you don't expect him to worry?"

"Funny girl."

"I try." She's feeling much better now that she's out of the infirmary.

They start to walk down the hall.

"Can I ask you one question?"

"Sure."

"How do you expect us to walk around Atlantis without being seen?"

"That's easy. I don't. We only have to get as far as the jumper bay."

Elizabeth stops walking. It takes Sheppard a moment (since he's busy watching out for other Atlantis team members) to realize that she's no longer walking next to him. He turns around to see her standing in the middle of the hallway, biting her lip, and glancing back in the direction of the infirmary.

Sheppard walks over and takes both her hands in his. He gives them a little squeeze when she continues to glance back the way they had come.

"Elizabeth, look at me."

She turns toward him reluctantly.

"You haven't been outside of this place since we got here. That can't be healthy."

"But..."

"But nothing. You have six – six whole people doing your job today. Doesn't that tell you something?"

"That I need to stay and make sure that they don't need something?"

"No." He heaves a big sigh and Elizabeth can't help but smile at how frustrated he looks.

_He looks kinda cute when he's frustrated._

_Yeah, but you think he's cute when he breathes._

Before she can ponder that realization, he continues.

"It means that you work too hard. Everyone needs down time and my goal today is to make sure you relax a little."

"I don't know..."

"Come on. Please? I've been working on this for two days."

_Oh, I'm in trouble now._

John was giving her this look that she just couldn't say no to. She is suddenly reminded of this amazingly friendly cat she had as a child. It would give her the same look whenever he wanted to be cuddled or fed or let outside to play.

"Okay..."

"Great! Let's go."

He scurries down the hall with her left hand gripped tightly in his right. Getting to the Jumper bay unseen is harder than Sheppard anticipates. But they soon make a game of evading the rest of Atlantis. They have to sneak around a few corners and duck into empty rooms. By the time they get into the jumper, they're both a little out of breath.

"You okay?"

"I'm fine." She gives him a smile to show that she's enjoying herself.

"Sure?"

"Sure."

"Alright then, let's go."

The doors open above them, letting in the sunlight. Elizabeth has one last moment of apprehension as the jumper starts to ascend. She looks over at Sheppard who gives her a wink. The jumper goes up through the roof and hovers over Atlantis. She realizes that John is giving her one last chance to change her mind.

_He's right, you know. You have been working too hard._

_I know, but there's so many people I'm responsible for._

_You won't do them any good by working yourself too hard._

_Just one day to really enjoy myself._

_Just one day._

Elizabeth gives John a brilliant smile, determined to have fun today.

"Let's go."

He matches her smile and the jumper takes off across the water.


	4. Surprises

**Ends and Means, Chapter 4**

The jumper skims over the water and Dr. Elizabeth Weir is sitting forward in her seat, enjoying every second. The craft is flying low, only a few yards over the water. Major John Sheppard knows he's showing off a little, but he likes seeing the look of pure joy on Elizabeth's face.

"You know where we're going, right?"

He turns to her with a look of mock indignation.

"Of course I do."

"I was just noticing that we don't seem to heading towards the mainland."

"That's good, 'cuz we're not going to the mainland."

"Really?!"

He smiles at her surprise.

"Really. Now relax. I know what I'm doing."

Elizabeth hesitates for the briefest moment before relaxing against her seat.

"Okay."

John sees that this isn't Dr. Weir, Leader of the Atlantis Expedition, whose massive responsibilities require her to question every decision. This is just Elizabeth, who is willing put her complete trust in him. He can't help but find that a little daunting.

"So what's in the bag?"

She motions towards the large duffel sitting between them.

"That, my dear, is part of the surprise."

"Really?"

"Really."

He laughs a little at her excitement. She sounds like an excited teenager. This is definitely not the Elizabeth Weir that she usually lets people see.

"Tell me what's in the bag."

"No."

"Please?"

"No."

"Pretty please?"

"I said no."

"Just tell me one thing in the bag."

"No! Were you like this during Christmas too?"

"Oh yeah. Used to drive my parents nuts."

That makes John laugh. He can just picture a little Elizabeth with pigtails, pestering her parents until they give in just to get a moment of peace.

"I usually got to open at least one present on Christmas Eve."

"Oh, I don't doubt that."

"I bet you used to drive your mom crazy by always finding your presents before Christmas."

"How do you know that?"

"Am I right?"

"Every Christmas and birthday." He chuckles at the memory. "Mom used to always hand me my present with this smug look on her face, thinking that she had gotten me this time. Then I would 'guess' what it was and she'd come this close to strangling me."

"Your poor mother." Elizabeth laughs. "You must have been an adorable kid."

"What?" He gives her a crooked smile. "You don't think I'm adorable now?"

Elizabeth blushes, then tries to change the subject. He lets her, but decides that he's going to try and make her blush like that at least once a day.

"I could order you to tell me what's in the bag."

"Nope. That won't work. I'm the pilot of this jumper and that means I'm in charge."

"That's not fair."

"Who said I was going to be fair? Actually..." He reaches into his pocket, pulls out a bandana, and hands it to her. "You need to put this on."

"You're serious?"

"Yup."

She shoots him one more suspicious look before putting the bandana over her eyes.

"No peeking!"

"I can't see anything, I promise."

He reaches over and tweaks her nose. She tries to swat at his hand and misses.

"Hey!"

"Just checking."

He looks out over the water and sees their destination coming into view. It's a small island - significantly smaller than the landmass the Athosians now called home. It had taken him two nights of flying to find it. But if Elizabeth's reaction is anywhere close to what he's hoping for, the sleepless nights will be well worth it.

She feels him slow the jumper for landing and straightens in her seat.

"Are we there?"

"Almost."

Sheppard makes the final approach and lands the jumper lightly in the grass. He gets up out of his seat as the rear hatch starts to open. He helps Elizabeth stand, liking the excuse of the blindfold to keep an arm wrapped tightly around her waist. They walk out the back of the jumper and he looks around to make sure the island is what he imagined it would be in the daylight. Satisfied with what he sees, he walks her over to his pre-chosen spot.

"Can I take the blindfold off?"

"Not quite yet."

John stands behind Elizabeth, making sure she's facing the way he wants. He wraps his left arm around her again as he leans forward to rest his cheek next to hers.

"Ready?"

"Ready."

He reaches up with his right hand and uncovers her eyes.

__


	5. Two Fish

**Ends and Means, Chapter 5**

Elizabeth has to remind herself to breathe. The sight in front of her is so beautiful, it's almost painful to see. That John is the one who has brought her here brings the sting of tears to her eyes.

They are standing on a grassy knoll. Behind them is a grove of trees which could pass for the mighty oaks of Earth - their leaves stirring in the constant breeze that blows over the water. In front of them is a stretch of white sand beach that has remained untouched by man for centuries. But what takes her breath away is what sits across the water. Atlantis sits on the horizon, shining like a beacon in the bright sun. The grandeur of the city cannot fully be appreciated when you're standing on her decks.

"Surprise." John whispers in her ear.

All she can do is hold on tight to arms that are wrapped around her. She wishes she could lose herself in this feeling, in this man, forever. But she can't keep reality from creeping into this world that he has created for her. She isn't a young girl with no cares or responsibilities. There are too many people counting on her. She knows that she can easily love this man, but that will bring complications she isn't prepared for. There is too much at stake, other people to consider.

As if sensing her slip away from him, John gives her a final squeeze before releasing her and stepping back. Elizabeth turns to face him. Her smile is both beautiful and sad.

"Thank you for this."

His eyes betray his disappointment and confusion. He reaches up to cup her cheek and is rewarded when she leans into his hand.

"Just...just enjoy yourself today, okay?"

"Okay."

The smile she gives him has lost some of its brilliance from the jumper, but he'll take it. He claps his hands, grins, and runs back to get the duffel. She can only stare in amazement as he spreads a blanket out on the grass below one of the trees. He motions for her to sit as he starts to pull food out of the bag. She is surprised to see standard picnic fare: cheese, crackers, fried chicken, and what looks like potato salad.

"How did you do this?"

He hands her the cutting board, cheese, and a knife. She starts cutting slices automatically.

"McKay got the food synthesizers working properly."

"Already?"

"Your suggestion worked. I guess that Donnelly, one of the chemists, is a closet chef. And you know how McKay is about food."

McKay had come into the infirmary a few days ago bemoaning the fact that, while they had finally found the food synthesizers, he couldn't get anything edible to actually come out. Since the Atlantis team could only bring a fixed amount of food on their trip, they had brought the supplies and scientists necessary to grow their own food. But deep down, everyone was hoping to find food synthesizers similar to what the Asgard used on their vessels. Rodney's first few attempts had, disappointingly, yielded food which tasted as awful as the Asgard pellets. Weir suggested that McKay find someone who actually knew how to make food, not just eat it.

"I even have wine." Sheppard's grin is infectious as he hands her a glass and clinks their glasses together. "To McKay."

"And Donnelly."

The food is surprisingly good. They don't quite have the textures right, but the flavors are very close. During the meal, they talk a little about how they grew up. But they are mostly content to enjoy their surroundings and each other's company.

It is much later when they are lying on the blanket, their heads resting on the now mostly empty duffel, that she decides to bring up their argument in the conference room. They are both staring up at the canopy of leaves above them and she feels more comfortable not looking him in the eye.

"About what happened before I collapsed."

"Yeah, I'm sorry about that. I shouldn't have yelled."

"And I shouldn't have yelled back..."

"I sense a 'but' coming."

"But that's not what concerns me."

"Then what does?"

Elizabeth sighs and turns to face him. This isn't a conversation she can have without looking at him. He mirrors her position.

"That wasn't the first time you blew up at someone."

He shrugs the shoulder that's off the ground.

"I let my temper get ahead of me. I don't take criticism well."

"That's a pocket answer and you know it."

"What do you want from me?"

"The flare ups. The yelling. That's not you, John."

"How do you know that?"

"I'm not sure how I know. But I think I'm right."

He starts to turn away, but she puts her hand on top of the one he has resting between them on the blanket. He stops and looks into her eyes.

"Talk to me. Tell me what's wrong."

"I'm a pilot."

Elizabeth waits for few seconds, but he doesn't continue.

"And..."

"I fly aircraft."

"And like to state the obvious."

He smiles a little and she hopes he's relaxed enough to tell her the truth.

"I fly – mostly alone. The biggest decision I usually had to make was how fast to take a landing."

"But as a pilot, you're responsible for the people in your aircraft."

"That's different."

"Why?"

"Because, in the end, all I have to do is fly the best I can."

"You mean that you're in total control of your fate."

"I guess that's one way of putting it."

"You're insecure of your ability to command."

"Okay...that's a way I'd rather you not put it."

She smiles and gives his hand a squeeze.

"You know you're a born leader, right?"

"Huh?"

"People follow you without even realizing that they're doing it."

"That doesn't mean I'll always make the right decisions."

"Nobody does."

"Not even you?"

"Well I did bring you on this expedition."

This is her attempt at lightening the mood and it works. They both chuckle.

"Yeah, you really screwed up there."

"It's not like you didn't warn me." She pauses for a moment. "But seriously, you have good instincts. The decisions you've made haven't been wrong so much as slightly misguided."

"You mean I've luckily managed not to screw up too much."

"That's one way of putting it."

"Is that how you see it?"

"No. I think you make decision to try and save everyone, make everyone equally happy."

"That doesn't sound so bad."

"No, it doesn't. But you have to realize that it's nearly impossible to save everyone all the time. Sometimes you have to do what's best for the most people and sacrifices have to be made."

"I'm not sure I can do that."

"I'm sure. And besides, you're not alone in the cockpit anymore. I'm here, along with the other members of Atlantis, to help make hard decisions."

"You mean mostly you."

"That's my job."

"A job you take too seriously."

"Uh-oh. Is it my turn to be given some friendly advice?"

"You work too hard."

"I have a lot to do."

"Making yourself sick isn't going to help anyone."

"It's not like I could control my appendix."

"But you were hurting and didn't do anything about it."

"I was busy."

"That's not a good excuse."

John switches the position of their hands and places his on top of hers.

"Look, I'll admit that I'm insecure about making decisions if you admit that you work too hard."

Elizabeth knows he's right. She really pushed it with her appendix. It seems like a minor thing, but she could have died.

"Okay. I'm just not used to being up front. I used to work in the background, brokering deals. It's hard to have so many people relying on me."

"So I guess we're just a pair of fish out of water then."

"Birds without wings."

"Cars without wheels."

"Monkeys without arms?"

"Trees without...uh...leaves?"

They both burst out laughing. Elizabeth hasn't felt this happy and relaxed in a long time.

"Thank you again, for today."

"My pleasure."

"I'll make you a deal. You make sure I'm not working too hard."

"And you make sure I'm not making bad decisions."

"Deal?"

"Deal."

The combination of the wine, the comfortable atmosphere, and her hand wrapped protectively in John's starts to lull Elizabeth to sleep. Her eyes flutter and close.

John stays awake and watches her sleep for a while. But soon his own sleepless nights catch up and overtake him.


	6. Okay for now

**End and Means, Chapter 6**

Major John Sheppard surfaces slowly from sleep into consciousness. He becomes aware of the warm body next to him and smiles. They have shifted in their sleep and Elizabeth is now wrapped tightly in his arms. Her head is resting on his shoulder with one hand lightly on his chest and the other at his hip.

_I could get used to waking up like this._

_Don't get ahead of yourself there, buddy._

His hold tightens around Elizabeth and she snuggles a little deeper into his embrace.

John sighs, remembering how she mentally pulled away from him earlier. Then he remembers his own inability to handle her being sick in the infirmary. He isn't used to dealing with women for too long after the chase.

_Oh come one. You've barely dealt with having to remember the women's names for longer than a few hours._

_This is going to be very different._

_Well, duh._

_She trusts me._

_I guess nobody's perfect._

_I'm going to need to be her friend, too._

_Yes John, women are good for being more than a quick roll in the hay._

_I don't think she wants to be chased._

_Anything worth having is worth fighting for._

_I'm gonna need to be patient._

_Not your strong suit, but it's doable. _

_I'm not sure I'm ready for this._

_Probably not. But I think that decision has already been made._

John looks over at the woman sleeping in his arms. She is even more beautiful in her sleep. The worry lines are gone, kept at bay by what he hopes are good dreams.

_Yeah. There's no backing out now._

_Just don't blow this._

_Not sure I can promise that, even to myself._

_Then try not to blow it too badly._

Elizabeth starts to stir in his arms. Before she is fully awake, he uses the opportunity to kiss the tip of her nose. He'll have to be satisfied with that for now. When he really does kiss her for the first time, he wants her fully conscious and aware of her actions.

Her eyes open to meet his. She isn't quite sure where she is.

"Morning, Sleepy Head."

He knows when she realizes how their bodies are positioned because her eyes open wide before she starts to pull away from him. It takes all of his willpower not to tighten his hold and kiss her senseless. Instead, he lets her sit up and lays back with his arms behind his head. She is nervously trying to smooth down her clothes and hair.

"Is it really morning?"

"No, but it is getting dark and I'm a lot less warm than I was earlier."

He grins when she blushes.

"So we should go?"

"Yeah, it's time to return to reality."

They get up and pack the blanket back in the duffel. He sees her take one final look at their little piece of paradise before she follows him up the rear ramp. She lets out a little sigh as the jumper lifts off the ground.

"Good day?" John asks.

"Great day."

"I'm glad."

"Can I ask you something?"

"Sure."

"I don't mean to sound ungrateful, but it's clear that you spent some time planning this for me. Why?"

"Two reasons. One, I felt guilty."

"Guilty about what?"

"Not realizing you were working too hard. That you were sick."

"There's nothing for you to feel guilty about. Nobody else noticed either."

"Maybe that's true. But I still felt like I let you down."

"Okay. And reason two?"

"I've kinda been avoiding the infirmary."

"I noticed that. I thought you were still angry about our little yelling match."

"That wasn't it. But you can add the pre-collapse argument to the list of why I felt guilty."

"So why were you avoiding me?"

"Because the whole you-almost-dying thing freaked me out a little."

"It's not like you've never done it."

"Yeah, but it's apparently harder to be the worrier than the worry-ee."

"Does that mean you're going to try harder not to end up in the infirmary yourself?"

"Doubt it."

"Didn't think so."

"By the time I realized that I was being a jerk by not visiting, I figured that it would take something big to make it up to you."

"You didn't have to. But I'm glad you did."

"Me too."

They sit in comfortable silence for the rest of the trip back to Atlantis. It's a slower flight since he's reluctant to end their day together. By the time he lands the jumper in the bay, it is fully dark and the hallways back to her quarters are deserted. They stand just outside her door.

"I'm glad nobody saw us."

"How come?"

"I don't want too many questions about where we've been."

"You're not planning on reporting the location of the island?"

"Nope, that's our little secret."

"Oh."

Elizabeth places her palm on the sensor and the door opens. She takes a half step into the doorway and turns back to him. Placing her hands on his shoulders for balance, she reaches up and brushes a light kiss on his cheek.

"You're a good friend John. Thank you."

She drops her arms, takes a step back, and the door closes between them.

John stands in the hall for a while, staring at the closed door. A slow grin spreads across his face as he finally turns toward his own quarters.

Friends. He could do that...for now at least.

The End

_Sorry if this isn't how some of you wanted this story to end. I don't want to get too ahead of the show's storyline. I want to see what they do about Simon in the upcoming episode "Home". _

_Thanks to everyone who has reviewed and encouraged me to keep going with this story. I have a random piece of fluff started, but I'm not sure if I'll get it out before I go on vacation next week. Thanks again and I promise I'll have more stuff for the Weir/Sheppard shippers out there soon._


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